Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3228
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58215
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2652 original size:73 final size:72
Alignment explanation
Indices: 2482--3749 Score: 590
Period size: 73 Copynumber: 16.6 Consensus size: 72
2472 AACATGTGAA
* *
2482 CTGAGGCTCAACTCACTTT-TCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACC
1 CTGAGGCTCAACTCA-TTTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAAAATACC
*
2546 TCAGCGTGTC
63 TCAACGTGTC
* *
2556 CTAAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAAATACCT
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAA-CAGAAATTG-AAAATACCT
2621 CAACGTGT-
64 CAACGTGTC
* * * *
2629 TTGAGGCTCAACTCATTTATCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTC-
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCA
*
2693 ATGTGTC
66 ACGTGTC
* * * * *
2700 TTGAGGCTCAACTTA-TTCTCGCAATATGAGTTGATTCTTTCAAAAACA-TAA-TGACAAA-ACA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATT-TTT-GAAAACAGAAATTGA-AAATACC
** *
2761 GAAATG-GAAAATAC
63 TCAACGTG----T-C
* * * *
2775 CTCGGTATGACCTGAGGCTCAACTCAACCTCTCGCAA-ATTGAG-TGATTTTTG-AAACAGAAAT
1 CT--G-A-G-GCTCA-ACTC-A-T----TTCTCGCAATA-TGAGTTGATTTTTGAAAACAGAAAT
* *
2837 TGAAATTACCTCAGCGTGTC
53 TGAAAATACCTCAACGTGTC
* * * *
2857 CTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA-ATTTGAAAACAGAAATTGAAATTATCTCA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCA
*
2921 GCGTGTC
66 ACGTGTC
* * *
2928 CTGAGGCTCAACTCATTTCTTGCAATATGAGTTGA-TTTTGAAAAAACAAAAATTGAAAAAGAGA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG--AAAACAGAAATTG--AAA-ATA
** * ** *
2992 AATGAAAATACCTC
61 CCTCAACGT--GTC
** * * ** * ** * * *
3006 AACATG-TCCTGAGGCTCAACTCAC-CTCT-TGCAATATGAGTTGATTTAGAAAACAGACATATA
1 --C-TGAGGCTCA-ACTCATTTCTCGCAATATG-AGT-TGA-TT--TTT-GAAAACAGAAAT-TG
* ** * *
3068 AAACAGAAATTGAAAGTGACTCAAAC
55 AAA-A-TACCTCAACGTG--T----C
** *
3094 ACGTGA-GC-CAAGGCTCAACTCACCTT-TCGCAATATGAG-TGATTTTTTTTGAAAGTAGAATT
1 -C-TGAGGCTCAA--CTC-A-T----TTCTCGCAATATGAGTTGA---TTTTTGAAAACAGAAAT
**
3155 TGAAAATACCTCGGCGTG-C
53 TGAAAATACCTCAACGTGTC
** ** *
3174 CCCAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG--AAAACAGAAATTGAAAATACCT
*
3239 CAGCGTGTC
64 CAACGTGTC
**
3248 CTGAGGCTCAACT-ACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAACAGTAATT
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG-AAAAC----A--G---A--AATT
3312 GAAAATA-CTCAACGTGTC
54 GAAAATACCTCAACGTGTC
* * ** * *
3330 TTGAGGATCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGACAACAGAAAATTGAAATTA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA----TTTTTGAAAACAG-AAATTGAAAATA
*
3395 CCTCAGCGTGTC
61 CCTCAACGTGTC
** *
3407 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAACAAAAATGAACAGGAATTGA
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAC----A-G---A--AATTG-
3471 AAAATACCTCAACGTGTC
55 AAAATACCTCAACGTGTC
* ** *
3489 TTGAGGCTCAACTCACCTCTCGACAATATGAGTTGATTTTCTTGAAAGCAGAAATTGAAAATACC
1 CTGAGGCTCAACTCATTTCTCG-CAATATGAGTTGA-TTT-TTGAAAACAGAAATTGAAAATACC
*
3554 TCAATGTGTC
63 TCAACGTGTC
* * *
3564 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCT
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAAAATACCT
**
3629 CCGCGTGTC
64 CAACGTGTC
* ** *
3638 CTGAGACTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACA-AAATTGAAAATTACCT
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTGAAAA-TACCT
*
3701 CAGCGTGTC
64 CAACGTGTC
*
3710 CTGAGGCTCAACTCATTTCTCGCGATATGAGTTGATTTTT
1 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
3750 TTTGGAAAGC
Statistics
Matches: 933, Mismatches: 146, Indels: 231
0.71 0.11 0.18
Matches are distributed among these distances:
70 45 0.05
71 123 0.13
72 87 0.09
73 133 0.14
74 133 0.14
75 47 0.05
76 24 0.03
77 48 0.05
78 11 0.01
79 8 0.01
80 17 0.02
81 20 0.02
82 63 0.07
83 50 0.05
84 23 0.02
85 10 0.01
86 23 0.02
87 26 0.03
88 15 0.02
89 4 0.00
90 8 0.01
91 6 0.01
92 1 0.00
93 6 0.01
94 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (72 bp):
CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAATACCTCA
ACGTGTC
Found at i:2874 original size:228 final size:230
Alignment explanation
Indices: 2527--3694 Score: 920
Period size: 228 Copynumber: 5.0 Consensus size: 230
2517 TTTTTTTGAC
* * * ** *
2527 AACAGAAATTGAAATTACCTCAGCGTGTCCTAAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAA-TGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
2592 TTTTGAAAAGCAGAAATTGAAAAATACCTCAACGTGTTTGAGGCTCAACTCATTTATCGCAATAT
65 TTTTGAAAAGCAGAAATTGAAAAATACCTCAACGTGTCTGAGGCTCAACTCATTTATCGCAATAT
* * * *
2657 GAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA-TGTGTCTTGAGGCTCAACTTA-TTCTC
130 AAGTTGAA-TTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTC
** *
2720 GCAATATGAGTTGATTCTTTCAAAAAC-ATAA-TGACAA
194 GCAATATGAGTTGATT-TTGAAAAAACAAAAATTGA-AA
* * *
2757 AACAGAAATGGAAAATACCTCGGTATGACCTGAGGCTCAACTCAACCTCTCGCAA-ATTGAG-TG
1 AACAGAAAT-GAAAATACCTCAGCATGTCCTGAGGCTCAACTC-ACCTCTCGCAATA-TGAGTTG
* * *
2820 ATTTTTG-AAA-CAGAAATTG-AAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAA
63 ATTTTTGAAAAGCAGAAATTGAAAAATACCTCAACGTGT-CTGAGGCTCAACTCATTTATCGCAA
*
2882 TATAAGTTGAATTTGAAAACAGAAATTGAAATTATCTCAGCGTGTCCTGAGGCTCAACTCATTTC
127 TATAAGTTGAATTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTC
*
2947 TTGCAATATGAGTTGATTTTGAAAAAACAAAAATTGAAA
192 TCGCAATATGAGTTGATTTTGAAAAAACAAAAATTGAAA
* * *
2986 AAGAGAAATGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA-T
1 AACAGAAATGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* * * **
3050 TTAGAAAACAGACATATAAAACAGAAATTG-AAAGTGA-CTCAAACACGTGAGCCAAGGCTCAAC
66 TTTG-AAA-AG----------CAGAAATTGAAAAAT-ACCTC--A-ACGTG-TCTGAGGCTCAAC
* * * ** * * *
3113 TCACCTT-TCGCAATATGAG-TGATTTTTTTTGAAAGTAGAATTTGAAAATACCTCGGCGTG-CC
114 TCA-TTTATCGCAATATAAGTTGA----ATTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCC
** ** *
3175 CCAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATT----
174 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAAACAAAAATTGAAA
*
3229 ----GAAAT-----TACCTCAGCGTGTCCTGAGGCTCAACT-ACCTCTCGCAATATGAGTTGATT
1 AACAGAAATGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* * * * ** *
3284 TTTGAAAAACATAAATTGAACAGTAATTGAAAATACTCAACGTGTCTTGAGGATCAACTCACCTC
66 TTTGAAAAGCAGAAATTGAA-A--AA-T----A-CCTCAACGTGTC-TGAGGCTCAACTCATTTA
* * *
3349 TCGCAATATGAGTTGATTTTTTTTTGACAACAGAAAATTGAAATTACCTCAGCGTGTCCTGAGGC
121 TCGCAATATAAGTTGA-----ATTTGAAAACAG-AAATTGAAATTACCTCAGCGTGTCCTGAGGC
** *
3414 TCAACTCACCTCTAGCAATATGAGTTGATTTTG--AAAACAAAAA-TG---
180 TCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAAACAAAAATTGAAA
* * * *
3459 AACAGGAATTGAAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGACAATATGAGTTG
1 AACA-GAAATG-AAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCG-CAATATGAGTTG
* *
3524 ATTTTCTTG-AAAGCAGAAATTG-AAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGC
63 A-TTT-TTGAAAAGCAGAAATTGAAAAATACCTCAACGTGTC-TGAGGCTCAACTCATTTATCGC
* * * * *
3587 AATATGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCCGCGTGTCCTGAGACTCAACTC
125 AATATAAGTTGA---ATTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTC
** *
3652 ACCTCTAGCAATATGAGTTGATTTTG-AAAAAC-AAAATTGAAA
187 ATTTCTCGCAATATGAGTTGATTTTGAAAAAACAAAAATTGAAA
3694 A
1 A
3695 TTACCTCAGC
Statistics
Matches: 781, Mismatches: 84, Indels: 141
0.78 0.08 0.14
Matches are distributed among these distances:
222 8 0.01
223 1 0.00
224 1 0.00
226 1 0.00
227 61 0.08
228 104 0.13
229 68 0.09
230 62 0.08
231 92 0.12
232 50 0.06
233 56 0.07
234 71 0.09
235 6 0.01
239 6 0.01
240 2 0.00
241 41 0.05
242 10 0.01
243 18 0.02
244 42 0.05
245 5 0.01
246 31 0.04
247 45 0.06
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (230 bp):
AACAGAAATGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTTGAAAAGCAGAAATTGAAAAATACCTCAACGTGTCTGAGGCTCAACTCATTTATCGCAATATA
AGTTGAATTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGC
AATATGAGTTGATTTTGAAAAAACAAAAATTGAAA
Found at i:2902 original size:71 final size:71
Alignment explanation
Indices: 2755--2985 Score: 279
Period size: 71 Copynumber: 3.2 Consensus size: 71
2745 ACATAATGAC
* * * ** * **
2755 AAAACAGAAATGGAAAATACCTCGGTATGACCTGAGGCTCAACTCAACCTCTCGCAA-ATTGAG-
1 AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTC-ATTTCTCGCAATA-TGAGT
2818 TGATTTTTG
64 TGA-TTTTG
*
2827 -AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTG
1 AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
*
2891 AATTTG
66 ATTTTG
* *
2897 AAAACAGAAATTGAAATTATCTCAGCGTGTCCTGAGGCTCAACTCATTTCTTGCAATATGAGTTG
1 AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
2962 ATTTTG
66 ATTTTG
*
2968 AAAAAACAAAAATTGAAA
1 --AAAACAGAAATTGAAA
2986 AAGAGAAATG
Statistics
Matches: 139, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
70 16 0.12
71 108 0.78
73 15 0.11
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (71 bp):
AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTG
ATTTTG
Found at i:3005 original size:157 final size:154
Alignment explanation
Indices: 2828--3748 Score: 815
Period size: 157 Copynumber: 5.9 Consensus size: 154
2818 TGATTTTTGA
* * ** *
2828 AACAGA-AATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA
1 AACAGAGAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* * *
2892 -ATTTGAAAACAGAAATTGAAATTATCTCAGCGTGTCCTGAGGCTCAACTCATTTCTTGCAATAT
66 TTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATAT
2956 GAGTTGATTTTGAAAAAACAAAAATTG
131 GAGTTGATTTTG--AAAAC-AAAATTG
* * * *
2983 AAAAAGAGAAATGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTG
1 -AACAGAGAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
* * * *
3048 ATTTAGAAAACAGACATAT-AAAACAGAAATTGAAAGTGA-CTCAAACACGTGAGCC-AAGGCTC
65 ATTT------------T-TGAAAACAGAAATTGAAA-TTACCTC--A-GCGTG-TCCTGAGGCTC
* **
3110 AACTCACCTT-TCGCAATATGAG-TGATTTT--------TTTTG
112 AACTCA-TTTCTCGCAATATGAGTTGATTTTGAAAACAAAATTG
** **
3144 AA-AGTAGAATTTGAAAATACCTCGGCGTG-CCCCAGGCTCAACTCACCTCTCGCAATATGAGTT
1 AACAG-AGAA-TTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
**
3207 GATTTTTGAAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACT-ACCTCTCGCA
64 GATTTTTG--AAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCA
3271 ATATGAGTTGATTTTTGAAAAACATAAATTG
127 ATATGAGTTGA-TTTTG-AAAACA-AAATTG
* * *
3302 AACAG-TAATTGAAAATA-CTCAACGTGTCTTGAGGATCAACTCACCTCTCGCAATATGAGTTGA
1 AACAGAGAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* ** *
3365 TTTTTTTTTGACAACAGAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGC
66 ----TTTTTGAAAACAG-AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGC
*
3430 AATATGAGTTGATTTTGAAAACAAAAATG
126 AATATGAGTTGATTTTGAAAACAAAATTG
*
3459 AACAG-GAATTGAAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGACAATATGAGTT
1 AACAGAGAATTG-AAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCG-CAATATGAGTT
* * ** *
3523 GATTTTCTTGAAAGCAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCA
64 GA-TTT-TTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCA
****
3588 ATATGAGTTGATTTTTTTGAC-------
127 ATATGAGTTGATTTTGAAAACAAAATTG
* ** * *
3609 AACAGA-AATTGAAATTACCTCCGCGTGTCCTGAGACTCAACTCACCTCTAGCAATATGAGTTGA
1 AACAGAGAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
*
3673 -TTTTGAAAAACA-AAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCGAT
66 TTTTTG-AAAACAGAAATTG-AAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAAT
3736 ATGAGTTGATTTT
129 ATGAGTTGATTTT
3749 TTTTGGAAAG
Statistics
Matches: 640, Mismatches: 69, Indels: 122
0.77 0.08 0.15
Matches are distributed among these distances:
145 11 0.02
146 74 0.12
147 18 0.03
148 19 0.03
149 36 0.06
150 29 0.05
155 7 0.01
156 46 0.07
157 129 0.20
158 32 0.05
159 78 0.12
160 81 0.13
161 18 0.03
170 20 0.03
171 3 0.00
172 8 0.01
173 27 0.04
174 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (154 bp):
AACAGAGAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATAT
GAGTTGATTTTGAAAACAAAATTG
Found at i:3039 original size:86 final size:87
Alignment explanation
Indices: 2897--3057 Score: 243
Period size: 86 Copynumber: 1.9 Consensus size: 87
2887 GTTGAATTTG
* * * * **
2897 AAAACAGAAATTGAAATTATCTCAGCGTGTCCTGAGGCTCAACTCATTTCTTGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTG
*
2962 ATTTTGAAAAAACAAAAATTGA
66 ATTTAGAAAAAACAAAAATTGA
*
2984 AAAAGAGAAA-TGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTG
3048 ATTTAGAAAA
66 ATTTAGAAAA
3058 CAGACATATA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 57 0.86
87 9 0.14
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (87 bp):
AAAACAGAAATTGAAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTG
ATTTAGAAAAAACAAAAATTGA
Found at i:3314 original size:233 final size:229
Alignment explanation
Indices: 2983--3749 Score: 793
Period size: 233 Copynumber: 3.3 Consensus size: 229
2973 ACAAAAATTG
* * *
2983 AAAAAGAGAAA-TG-AAAATACCTCAACATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
1 AAAAACAGAAATTGAAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* ** *
3046 TGA-TTTAGAAAACAGACATATAAAACAGAAATTGAAAGTGACTCAAACACGTGAGCCAAGGCTC
66 TGATTTTTGAAAACAGA-A-ATTGAACAGTAATTGAAAGTGACTC--A-ACGTG-G-C-AGGCTC
* * * *
3110 AACTCACCTTTCGCAATATGAG-TGATTTTTTTTGA-AAGTAGAATTTGAAAATACCTCGGCGTG
123 AACTCACCTTTCGCAATATGAGTTGATTTTTTTTGACAA-CAGAAATTGAAATTACCTCAGCGTG
** *
3173 -CCCCAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
187 TCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGA
* *
3216 AAAAACAGAAATTG-AAATTACCTCAGCGTGTCCTGAGGCTCAACT-ACCTCTCGCAATATGAGT
1 AAAAACAGAAATTGAAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * * *
3279 TGATTTTTGAAAAACATAAATTGAACAGTAATTGAAAAT-ACTCAACGTGTCTTGAGGATCAACT
66 TGATTTTTG-AAAACAGAAATTGAACAGTAATTGAAAGTGACTCAACGTGGC---AGGCTCAACT
*
3343 CACCTCTCGCAATATGAGTTGATTTTTTTTTGACAACAGAAAATTGAAATTACCTCAGCGTGTCC
127 CACCTTTCGCAATATGAGTTGA-TTTTTTTTGACAACAG-AAATTGAAATTACCTCAGCGTGTCC
3408 TGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAACAA
190 TGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG------A
* *
3454 AAATGAACAGGAATTGAAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGACAATATG
1 AAA--AACAGAAATTGAAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCG-CAATATG
* * ** * * *
3519 AGTTGATTTTCTTGAAAGCAGAAATTGAA-AATACCTCAATGTG--T---C-TTG-AGGCTCAAC
63 AGTTGA-TTT-TTGAAAACAGAAATTGAACAGTAATTGAAAGTGACTCAACGTGGCAGGCTCAAC
* *
3576 TCA-TTTCTCGCAATATGAGTTGA-TTTTTTTGACAACAGAAATTGAAATTACCTCCGCGTGTCC
126 TCACCTT-TCGCAATATGAGTTGATTTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCC
*
3639 TGAGACTCAACTCACCTCTAGCAATATGAGTTGATTTTG-
190 TGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGA
* * ** *
3678 AAAAACA-AAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCGATATGAGT
1 AAAAACAGAAATTGAAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
3742 TGATTTTT
66 TGATTTTT
3750 TTTGGAAAGC
Statistics
Matches: 461, Mismatches: 48, Indels: 65
0.80 0.08 0.11
Matches are distributed among these distances:
218 2 0.00
219 3 0.01
220 12 0.03
221 41 0.09
222 4 0.01
224 3 0.01
227 1 0.00
229 31 0.07
230 4 0.01
231 74 0.16
232 45 0.10
233 80 0.17
234 62 0.13
235 7 0.02
238 5 0.01
239 1 0.00
240 10 0.02
241 28 0.06
242 9 0.02
243 20 0.04
244 16 0.03
245 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (229 bp):
AAAAACAGAAATTGAAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTGAAAACAGAAATTGAACAGTAATTGAAAGTGACTCAACGTGGCAGGCTCAACTCACC
TTTCGCAATATGAGTTGATTTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGC
TCAACTCACCTCTAGCAATATGAGTTGATTTTGA
Found at i:20450 original size:21 final size:21
Alignment explanation
Indices: 20424--20465 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20414 TTTATGATGA
20424 AAAAATAA-ATATTTTATATAT
1 AAAAATAATA-ATTTTATATAT
*
20445 AAAAATAATAATTTTTTATAT
1 AAAAATAATAATTTTATATAT
20466 TTTTCCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAATAATAATTTTATATAT
Found at i:20461 original size:23 final size:22
Alignment explanation
Indices: 20403--20465 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
20393 ATTTATCGTT
20403 AATATAATTTCTTTATGATGAAAA
1 AATATAATTT-TTTAT-ATGAAAA
*
20427 AATA-AATATTTTATAT-ATAAA
1 AATATAATTTTTTATATGA-AAA
20448 AATAATAATTTTTTATAT
1 AAT-ATAATTTTTTATAT
20466 TTTTCCTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 8 0.24
22 6 0.18
23 15 0.44
24 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (22 bp):
AATATAATTTTTTATATGAAAA
Found at i:21501 original size:4 final size:4
Alignment explanation
Indices: 21492--21516 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
21482 CCTATTCTAG
21492 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
21517 TATATTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:22217 original size:21 final size:21
Alignment explanation
Indices: 22177--22217 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22167 TTTTTACACG
* *
22177 ATATTTTACATGTTACTTTTT
1 ATATTTTAAATGTTAATTTTT
*
22198 ATATTTTAAATTTTAATTTT
1 ATATTTTAAATGTTAATTTT
22218 ATAAATTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (21 bp):
ATATTTTAAATGTTAATTTTT
Found at i:22328 original size:20 final size:20
Alignment explanation
Indices: 22303--22362 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 20
22293 TTATTTAAAA
*
22303 TTAAAT-TTTTTATATATTAT
1 TTAAATATTTCTATAT-TTAT
22323 TTAAATATTTCTATATTTA-
1 TTAAATATTTCTATATTTAT
*
22342 -TAAATATAT-TATATGTTAT
1 TTAAATATTTCTATAT-TTAT
22361 TT
1 TT
22363 TCAAAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 5 0.15
18 11 0.32
20 10 0.29
21 8 0.24
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TTAAATATTTCTATATTTAT
Found at i:22501 original size:24 final size:24
Alignment explanation
Indices: 22452--22498 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
22442 TTATCAAAAA
*
22452 AAATTTAATTTAATTGTTCATATT
1 AAATTTAAATTAATTGTTCATATT
*
22476 AAATTTAAATTAATT-TTTATATT
1 AAATTTAAATTAATTGTTCATATT
22499 TAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
AAATTTAAATTAATTGTTCATATT
Found at i:26925 original size:84 final size:84
Alignment explanation
Indices: 26708--27534 Score: 1272
Period size: 84 Copynumber: 9.9 Consensus size: 84
26698 CTTTCGTCTA
* * *
26708 CTCCACTACTGCTTAGGGAGATAAGA-CTGG---ATGT-GATCTGCTCCATTACTGCTTAGGGAG
1 CTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCG-TCTGCTCCACTACTGCTTAGGGAG
* * * *
26768 ATAAGATCTGTGGTTTTAATCCG
65 ATAAGA-CT-T-GATGTGATCTG
* ** * *
26791 CTCCACTGCAACTTCAGGGAGATAGGAT-TGGTTTCTTTCGTCTGCTCCACTACTTCTTAGGGAG
1 CTCCACTACTGCTT-AGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAG
*
26855 ATAAGACTGGATGTGATCTG
65 ATAAGACTTGATGTGATCTG
*
26875 CTCCATTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
26940 TAAGACTTGATGTGATCTG
66 TAAGACTTGATGTGATCTG
*
26959 CTCCACTACTACTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
*
27024 TAAGACTTCATGTGATCTG
66 TAAGACTTGATGTGATCTG
* *
27043 CTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCTACTACTGCTTAAGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
*
27108 TAAGACTTGATGCGATCTG
66 TAAGACTTGATGTGATCTG
*
27127 CTCCACTACTGCTTAAGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
27192 TAAGACTTGATGTGATCTG
66 TAAGACTTGATGTGATCTG
*
27211 CTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTTGTCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
*
27276 TAAGACCTGATGTGATCTG
66 TAAGACTTGATGTGATCTG
* * * * *
27295 CTCCACTACTACTCAGGGAGATAAGATCTGGTTTCTTTTGTCTGCTCCACTACTACTTAGAGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
27360 TAAGACTTGATGTGATCTG
66 TAAGACTTGATGTGATCTG
* *
27379 CTCCACTACTGCTTAGAGAGATAAGATCTGGTTTCTTTTGTCTGCTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
27444 TAAGACTTGATGTGATCTG
66 TAAGACTTGATGTGATCTG
* *
27463 CTCCACTACTGGC-TAGGGAGATAAGATCTGGTTTCTTTTGTCTGCTCCACTACTACTTAGGGAG
1 CTCCACTACT-GCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAG
27527 ATAAGACT
65 ATAAGACT
27535 GTTGGCTTCA
Statistics
Matches: 689, Mismatches: 47, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
83 23 0.03
84 631 0.92
85 2 0.00
86 2 0.00
87 30 0.04
88 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (84 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGGTTTCTTTCGTCTGCTCCACTACTGCTTAGGGAGA
TAAGACTTGATGTGATCTG
Found at i:27799 original size:88 final size:87
Alignment explanation
Indices: 27705--28483 Score: 800
Period size: 88 Copynumber: 8.8 Consensus size: 87
27695 GTCGTTAGTA
* * * * *
27705 CAGGAAGGCAAGATCTGCAATC-TCTGACCTGCTCCACTACAACCGAGGGAGGCAAGACTTGTGT
1 CAGGAAGGCAAGATCTGCTATCTTC-AACCAGCTCCACTACAACCGAGAGAGGCAAG-TTTGTGT
*
27769 CTTTGATCTGCTTCGCTGTCAATA
64 CTTTGATCTGCTTCGCTGTCAATG
** * *
27793 CAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTGTGTC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAA-GTTTGTGTC
* * * * *
27858 TTCGACCTACTTCACTGTCAATA
65 TTTGATCTGCTTCGCTGTCAATG
* *
27881 CAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTGTC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAA-GTTTGTGTC
* *
27946 TTCGACCTGCTTCGCTGTCAATG
65 TTTGATCTGCTTCGCTGTCAATG
** * *
27969 CAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATG-GAGGCAATGTTTTCTA
1 CAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAA-G--TT-TG
* **
28033 TTTCTTTGATCTG-TTCTTTGTCAATG
61 TGTCTTTGATCTGCTTCGCTGTCAATG
* ** * *
28059 TAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCTACTACAACCGAGAGAGGCAATGTTTGTGTC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAA-GTTTGTGTC
* *
28124 TTTGACCTGCTTCACTGTCAATG
65 TTTGATCTGCTTCGCTGTCAATG
* * * *
28147 CAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGAAAGGTTTGTGTC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAA-GTTTGTGTC
* **
28212 TTCGATCTGCTTCGCTGTCAGGG
65 TTTGATCTGCTTCGCTGTCAATG
* * * ** *
28235 CAGGAAGGCAAGATCTGTTGTCTTCAAACAGCTCTGCTACAACCGAGAGAGGTAAGGTTT-TGT-
1 CAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAA-GTTTGTGTC
* *
28298 TTTCGATCTGCTTCGCTGTTAACG
65 TTT-GATCTGCTTCGCTGTCAATG
* * ** *
28322 CAGGAATGCAAGATCTGCTATCTTTAACCAGCTCTGCTACAACTGAGAGAGGCAAGGTTT-TGT-
1 CAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAA-GTTTGTGTC
* * *
28385 TTTCGATCCGCTTCGCTATTAATG
65 TTT-GATCTGCTTCGCTGTCAATG
* * * *
28409 CAGGAAGGCAAGATCTACTATCTTTAACCAGCTCCACTACAACCGATG-GAGGCAAGGATCTGTT
1 CAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGA-GAGAGGCAA-G-TTTGTG
28473 TCTTTGATCTG
63 TCTTTGATCTG
28484 TTTTCTGGGG
Statistics
Matches: 597, Mismatches: 81, Indels: 25
0.85 0.12 0.04
Matches are distributed among these distances:
86 2 0.00
87 159 0.27
88 350 0.59
89 12 0.02
90 63 0.11
91 11 0.02
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (87 bp):
CAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGTTTGTGTCT
TTGATCTGCTTCGCTGTCAATG
Found at i:27802 original size:44 final size:45
Alignment explanation
Indices: 27597--27808 Score: 161
Period size: 44 Copynumber: 4.8 Consensus size: 45
27587 TTAATCTGCT
* *
27597 ATCTACTTCGCTGTCAATACAGGAAGGTAAGATCTGCTATCTTT-
1 ATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTATCTTTG
* * * *
27641 AGTCTGCTCCACTGTCAGTACAGGAAGGCAAGA-CTGGCT-TCTTCG
1 A-TCTGCTTCGCTGTCAATACAGGAAGGCAAGATCT-GCTATCTTTG
* * * * *
27686 ATCTACTTCG-TCGTTAGTACAGGAAGGCAAGATCTGCAATCTCTG
1 ATCTGCTTCGCT-GTCAATACAGGAAGGCAAGATCTGCTATCTTTG
* * * * * * *
27731 ACCTGCTCCACT-ACAA-CCGAGGGAGGCAAGA-CTTG-TGTCTTTG
1 ATCTGCTTCGCTGTCAATAC-AGGAAGGCAAGATC-TGCTATCTTTG
27774 ATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCT
1 ATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCT
27809 ATTGTCTTCA
Statistics
Matches: 125, Mismatches: 31, Indels: 24
0.69 0.17 0.13
Matches are distributed among these distances:
43 17 0.14
44 63 0.50
45 44 0.35
46 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (45 bp):
ATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTGCTATCTTTG
Found at i:27860 original size:43 final size:43
Alignment explanation
Indices: 27811--27948 Score: 131
Period size: 43 Copynumber: 3.2 Consensus size: 43
27801 CAAGATCTAT
27811 TGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTG
* * * * *
27854 TGTCTTCGACCTA-CTTCACTGTCA-ATACAG-GA-AGGCAAGATCTG
1 TGTCTTCAACC-AGCTCCAC---CACA-ACCGAGAGAGGCAAGGTTTG
* *
27898 CTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTG
1 -TGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTG
27942 TGTCTTC
1 TGTCTTC
27949 GACCTGCTTC
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
42 4 0.05
43 25 0.34
44 22 0.30
45 17 0.23
46 5 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (43 bp):
TGTCTTCAACCAGCTCCACCACAACCGAGAGAGGCAAGGTTTG
Found at i:27978 original size:44 final size:43
Alignment explanation
Indices: 27754--27980 Score: 140
Period size: 44 Copynumber: 5.2 Consensus size: 43
27744 CAACCGAGGG
** * *
27754 AGGCAAGACTTGTGTCTTTGATCTGCTTCGCTGTCAATACAGGA
1 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAAT-CAGGA
* * * * * ** *
27798 AGGCAAGATCTAT-TGTCTTCAACCAGCTCCAC-CACAA-CCGAGA
1 AGGCAAGGT-T-TGTGTCTTCGACCTGCTTCGCTGTCAATCAG-GA
* *
27841 GAGGCAAGGTTTGTGTCTTCGACCTACTTCACTGTCAATACAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAAT-CAGGA
* * * * * * *
27886 AGGCAAGATCTGCTGTCTTCAACCAGCTCCGCT-ACAA-CCGAGA
1 AGGCAAGGTTTG-TGTCTTCGACCTGCTTCGCTGTCAATCAG-GA
27929 GAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAAT-CAGGA
27974 AGGCAAG
1 AGGCAAG
27981 ATCTGCTATC
Statistics
Matches: 135, Mismatches: 34, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
42 5 0.04
43 37 0.27
44 55 0.41
45 33 0.24
46 5 0.04
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.25
Consensus pattern (43 bp):
AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATCAGGA
Found at i:28111 original size:266 final size:263
Alignment explanation
Indices: 27705--28465 Score: 956
Period size: 266 Copynumber: 2.9 Consensus size: 263
27695 GTCGTTAGTA
* * * ** * *
27705 CAGGAAGGCAAGATCTGCAATCTCTGACCTGCTCCACTACAACCGAGGGAGGCAAGACTTGTGTC
1 CAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTACAACCGA-GGAGGCAAGTTTTTTTTC
* * *
27770 TTTGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAA
65 TTTGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCTACTACAA
* *
27835 CCGAGAGAGGCAAGGTTTGTGTCTTCGACCTACTTCACTGTCAATACAGGAAGGCAAGATCTGCT
130 CCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCT
27900 GTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTC
195 GTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTC
*
27965 AATG
260 AAGG
*
27969 CAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATGGAGGCAATGTTTTCTAT
1 CAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTACAACCGA-GGAGGCAA-GTTTT-T-T
** *
28034 TTCTTTGATCTG-TTCTTTGTCAATGTAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCTACTA
62 TTCTTTGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCTACTA
* *
28098 CAACCGAGAGAGGCAATGTTTGTGTCTTTGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCT
127 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCT
* * *
28163 GTTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGAAAGGTTTGTGTCTTCGATCTGCTTCGCT
192 GCTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCT
*
28228 GTCAGGG
257 GTCAAGG
* * ** * ** * * *
28235 CAGGAAGGCAAGATCTGTTGTCTTCAAACAGCTCTGCTACAACCGAGAGAGGTAAGGTTTTGTT-
1 CAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTACAACCGAG-GAGGCAAGTTTTTTTTC
* * * * ** * * *
28299 TTCGATCTGCTTCGCTGTTAACGCAGGAATGCAAGATCTGCTATCTTTAACCAGCTCTGCTACAA
65 TTTGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCTACTACAA
* * * * * *
28364 CTGAGAGAGGCAAGGTTT-TGTTTTCGATCC-GCTTCGCTATTAATGCAGGAAGGCAAGATCTAC
130 CCGAGAGAGGCAAGGTTTGTGTCTTCGA-CCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGC
* * *
28427 TATCTTTAACCAGCTCCACTACAACCGATG-GAGGCAAGG
194 TGTCTTCAACCAGCTCCGCTACAACCGA-GAGAGGCAAGG
28466 ATCTGTTTCT
Statistics
Matches: 430, Mismatches: 60, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
262 76 0.18
263 65 0.15
264 51 0.12
265 8 0.02
266 218 0.51
267 12 0.03
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (263 bp):
CAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTACAACCGAGGAGGCAAGTTTTTTTTCT
TTGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCTACTACAAC
CGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGCTG
TCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCA
AGG
Found at i:28213 original size:43 final size:43
Alignment explanation
Indices: 28077--28214 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 43
28067 CAAGATCTAT
* *
28077 TGTCTTCAACCAGCTCTACTACAACCGAGAGAGGCAATGTTTG
1 TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
** * * * * * *
28120 TGTCTTTGACCTGCTTCACTGTCAA-TGCAG-GAAGGCAAGATCTG
1 TGTCTTCAACCAGCTCCACT-ACAACCG-AGAG-AGGCAAGGTTTG
* *
28164 TTGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGAAAGGTTTG
1 -TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
28208 TGTCTTC
1 TGTCTTC
28215 GATCTGCTTC
Statistics
Matches: 69, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
43 24 0.35
44 28 0.41
45 17 0.25
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (43 bp):
TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
Found at i:28250 original size:354 final size:349
Alignment explanation
Indices: 27705--28464 Score: 997
Period size: 354 Copynumber: 2.2 Consensus size: 349
27695 GTCGTTAGTA
* * * *
27705 CAGGAAGGCAAGATCTGCAATC-TCTGACCTGCTCCACTACAACCGAGGGAGGCAAGACTTGTGT
1 CAGGAAGGCAAGATCTACTATCTTC-AACCAGCTCCACTACAACCGA-GGAGGCAAGACTTGTGT
* *
27769 CTTTGATCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACA
64 CTTTGACCTGCTTCACTGTCAATACAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACA
* *
27834 ACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTACTTCACTGTCAATACAGGAAGGCAAGATCTGC
129 ACCGAGAGAGGAAAGGTTTGTGTCTTCGACCTACTTCACTGTCAAGACAGGAAGGCAAGATCTGC
*
27899 TGTCTTCAACCAGCTCCGCTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGT
194 TGTCTTCAAACAGCTCCGCTACAACCGAGAGAGGCAAGGTTT-TGTCTTCGACCTGCTTCGCTGT
* * * *
27964 CAATGCAGGAAGGCAAGATCTGCTATCTTTGACCAGCTCCACTGCAACCGATG-GAGGCAATGTT
258 CAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGA-GAGAGGCAAGGTT
* ** *
28028 TTCTATTTCTTTGATCTG-TTCTTTGTCAATG
322 TTCT-TTTC---GATCCGCTTCGCTATCAATG
* * * * *
28059 TAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCTACTACAACCGAGAGAGGCAATG-TTTGTGT
1 CAGGAAGGCAAGATCTACTATCTTCAACCAGCTCCACTACAACCGAG-GAGGCAA-GACTTGTGT
* * * *
28123 CTTTGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCGCTACA
64 CTTTGACCTGCTTCACTGTCAATACAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACA
* * * * * *
28188 ACCGAGAGAGGAAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAGGGCAGGAAGGCAAGATCTGT
129 ACCGAGAGAGGAAAGGTTTGTGTCTTCGACCTACTTCACTGTCAAGACAGGAAGGCAAGATCTGC
* * * * *
28253 TGTCTTCAAACAGCTCTGCTACAACCGAGAGAGGTAAGGTTTTGTTTTCGATCTGCTTCGCTGTT
194 TGTCTTCAAACAGCTCCGCTACAACCGAGAGAGGCAAGGTTTTGTCTTCGACCTGCTTCGCTGTC
* ** *
28318 AACGCAGGAATGCAAGATCTGCTATCTTTAACCAGCTCTGCTACAACTGAGAGAGGCAAGGTTTT
259 AACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTT
* *
28383 GTTTTCGATCCGCTTCGCTATTAATG
324 CTTTTCGATCCGCTTCGCTATCAATG
*
28409 CAGGAAGGCAAGATCTACTATCTTTAACCAGCTCCACTACAACCGATGGAGGCAAG
1 CAGGAAGGCAAGATCTACTATCTTCAACCAGCTCCACTACAACCGA-GGAGGCAAG
28465 GATCTGTTTC
Statistics
Matches: 352, Mismatches: 48, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
349 6 0.02
350 57 0.16
351 1 0.00
352 5 0.01
353 77 0.22
354 203 0.58
355 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (349 bp):
CAGGAAGGCAAGATCTACTATCTTCAACCAGCTCCACTACAACCGAGGAGGCAAGACTTGTGTCT
TTGACCTGCTTCACTGTCAATACAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCACCACAAC
CGAGAGAGGAAAGGTTTGTGTCTTCGACCTACTTCACTGTCAAGACAGGAAGGCAAGATCTGCTG
TCTTCAAACAGCTCCGCTACAACCGAGAGAGGCAAGGTTTTGTCTTCGACCTGCTTCGCTGTCAA
CGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTTCT
TTTCGATCCGCTTCGCTATCAATG
Found at i:29097 original size:108 final size:108
Alignment explanation
Indices: 28908--29103 Score: 286
Period size: 108 Copynumber: 1.8 Consensus size: 108
28898 GAAAAATGCT
28908 TGAAAAAAATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
1 TGAAAAAAATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
28973 CAATCAAGACAGCAAATTTTGCTGAGATATGAGATGTATAAGA
66 CAATCAAGACAGCAAATTTTGCTGAGATATGAGATGTATAAGA
* * * * ** *
29016 TGAAAAAGATTATCACAATGGATAAGATGGAAA-TTTGTTGAGAGCAAAGCTCTAAATGAATAAA
1 TGAAAAAAATTATCAAAATGGACAAAAT-GAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAA
* * *
29080 TTAATCAATATAGCAAATTTTGCT
65 TCAATCAAGACAGCAAATTTTGCT
29104 AGAATATAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
108 73 0.95
109 4 0.05
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (108 bp):
TGAAAAAAATTATCAAAATGGACAAAATGAAATTTTGTTGAGAGCAAAGCTCTAAACAAACAAAT
CAATCAAGACAGCAAATTTTGCTGAGATATGAGATGTATAAGA
Found at i:29167 original size:45 final size:43
Alignment explanation
Indices: 29069--29169 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 43
29059 GCAAAGCTCT
* * * *
29069 AAATGAATAAATTAATCAATATAGCAAATTTTGCTAGAATATA
1 AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATAAA
* *
29112 AAATGAGAATAAATTAATCAAGATGGCATATTTTGTCAAAAATACAA
1 AAAT--GAATAAATTAATCAAGATAGCAAATTTTG-CAAAAATA-AA
29159 AAATGAATAAA
1 AAATGAATAAA
29170 ATGGAAATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.08
45 33 0.69
46 6 0.12
47 5 0.10
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (43 bp):
AAATGAATAAATTAATCAAGATAGCAAATTTTGCAAAAATAAA
Found at i:29484 original size:34 final size:34
Alignment explanation
Indices: 29433--29511 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
29423 TCACCTTGGC
* * *
29433 CTCTCCTTTTTCTTTTTTCATTC-TTCCTTTTTTT
1 CTCTTCTTTTTCGTTTTT-ATTCTTTCCGTTTTTT
* * *
29467 CTTTTCTTTTTCGTTTTTTTTCTTTTCGTTTTTT
1 CTCTTCTTTTTCGTTTTTATTCTTTCCGTTTTTT
29501 CTCTTCTTTTT
1 CTCTTCTTTTT
29512 TTTCAAGTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
33 3 0.08
34 34 0.92
ACGTcount: A:0.01, C:0.22, G:0.03, T:0.75
Consensus pattern (34 bp):
CTCTTCTTTTTCGTTTTTATTCTTTCCGTTTTTT
Found at i:29492 original size:15 final size:15
Alignment explanation
Indices: 29463--29505 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
29453 TTCTTCCTTT
29463 TTTTCTTTTCTTTTTCG
1 TTTT-TTTTC-TTTTCG
29480 TTTTTTTTCTTTTCG
1 TTTTTTTTCTTTTCG
*
29495 TTTTTTCTCTT
1 TTTTTTTTCTT
29506 CTTTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 16 0.64
16 5 0.20
17 4 0.16
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (15 bp):
TTTTTTTTCTTTTCG
Found at i:29982 original size:16 final size:15
Alignment explanation
Indices: 29954--29997 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
29944 GAGGTTCTTT
*
29954 TATTTTTTA-TTTTC
1 TATTTTTTACTTTTA
29968 TCATTTTTTACTTTTA
1 T-ATTTTTTACTTTTA
*
29984 TTTTTTTTACTTTT
1 TATTTTTTACTTTT
29998 TTCGCCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 1 0.04
15 20 0.77
16 5 0.19
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTTTACTTTTA
Found at i:31410 original size:62 final size:63
Alignment explanation
Indices: 31308--31428 Score: 199
Period size: 62 Copynumber: 1.9 Consensus size: 63
31298 CTAAACTCAA
* *
31308 CGTACTTTTTAGATTTTAGGAAATTAATTGTATGCAATGAAGTGTAATGTTGATGCATGAATG
1 CGTACTTTTTAGATTTTAGGAAATTAATTGTATGCAATGAAATGTAATGTTAATGCATGAATG
* *
31371 CGTA-TTTTTGGATTTTAGGAAATTTATTGTATGCAATGAAATGTAATGTTAATGCATG
1 CGTACTTTTTAGATTTTAGGAAATTAATTGTATGCAATGAAATGTAATGTTAATGCATG
31429 GAAAAGAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
62 50 0.93
63 4 0.07
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.41
Consensus pattern (63 bp):
CGTACTTTTTAGATTTTAGGAAATTAATTGTATGCAATGAAATGTAATGTTAATGCATGAATG
Found at i:32374 original size:15 final size:14
Alignment explanation
Indices: 32349--32383 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
32339 TGCAGCAGTA
32349 TACCAAGCTTAAAC
1 TACCAAGCTTAAAC
32363 TACCACAGCTTAAAC
1 TACCA-AGCTTAAAC
32378 TACCAA
1 TACCAA
32384 AATCAAGACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.43, C:0.31, G:0.06, T:0.20
Consensus pattern (14 bp):
TACCAAGCTTAAAC
Found at i:33172 original size:127 final size:126
Alignment explanation
Indices: 32986--33225 Score: 310
Period size: 127 Copynumber: 1.9 Consensus size: 126
32976 TTATTTTAAT
* *
32986 TTTAAAAGGATATTCGGTTATTTAGGTCAACGAGAAAAATCGAAGCCCAGTAAGTTAGGGCACGA
1 TTTAAAAGGATATTCGGCTATTCAGGTCAACGAGAAAAATCGAAGCCCAGTAAGTTAGGGCACGA
* *
33051 TT-TCTCGAATTTTCTAAATAT-AGA-ATATTGCCTTTATTTTTGAAATTTTATACGTTTGGAAA
66 TTCT-TCGAATTTCCTAAA-ATGAGAGATATTGCC-TTA-TTTTAAAATTTTATACGTTTGGAAA
** * *
33113 TTTAAAAGGATATTTTGCTATTCAGGTTTAACGAG-AAAATCG-AGACCCAGTAAGTTAGGGTAC
1 TTTAAAAGGATATTCGGCTATTCAGG-TCAACGAGAAAAATCGAAG-CCCAGTAAGTTAGGGCAC
*
33176 GATTCTTCGAATTTCCTAAAATGCGAGATATTGCCTTATTTTAAAATTTT
64 GATTCTTCGAATTTCCTAAAATGAGAGATATTGCCTTATTTTAAAATTTT
33226 CTTTTTGAAT
Statistics
Matches: 99, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
126 15 0.15
127 68 0.69
128 16 0.16
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (126 bp):
TTTAAAAGGATATTCGGCTATTCAGGTCAACGAGAAAAATCGAAGCCCAGTAAGTTAGGGCACGA
TTCTTCGAATTTCCTAAAATGAGAGATATTGCCTTATTTTAAAATTTTATACGTTTGGAAA
Found at i:36140 original size:6 final size:6
Alignment explanation
Indices: 36129--36176 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
36119 AATTGATTAT
* *
36129 ATTAAA ATTAAA ATTAAA ATTAAA A-TATAA A-TATA ATTAAA AATAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTA-AA ATTAAA ATTAAA ATTAAA
36176 A
1 A
36177 AATATATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATTAAA
Found at i:36166 original size:23 final size:23
Alignment explanation
Indices: 36140--36186 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
36130 TTAAAATTAA
* *
36140 AATTAAAATTAAAATATAAATAT
1 AATTAAAAATAAAAAATAAATAT
*
36163 AATTAAAAATAAAAAATATATAT
1 AATTAAAAATAAAAAATAAATAT
36186 A
1 A
36187 TTTATTAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATTAAAAATAAAAAATAAATAT
Found at i:42353 original size:18 final size:17
Alignment explanation
Indices: 42321--42354 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42311 TATTTTCAAA
*
42321 TTATAAAGTAAATTAAT
1 TTATAAAGAAAATTAAT
42338 TTATAAAGAAAAATTAA
1 TTATAAAG-AAAATTAA
42355 GAGCGAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
TTATAAAGAAAATTAAT
Found at i:42560 original size:15 final size:17
Alignment explanation
Indices: 42540--42577 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
42530 ATTTTTTTAA
42540 AAATTATAAAAAT-AT-
1 AAATTATAAAAATCATG
*
42555 AAATTATTAAAATCATG
1 AAATTATAAAAATCATG
42572 AAATTA
1 AAATTA
42578 CTTTTTAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
AAATTATAAAAATCATG
Found at i:43020 original size:17 final size:17
Alignment explanation
Indices: 42995--43034 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
42985 ATGTTTCTAT
*
42995 TATTATTTATTTGTATG
1 TATTTTTTATTTGTATG
*
43012 TATTTTTTATTTTTATG
1 TATTTTTTATTTGTATG
*
43029 AATTTT
1 TATTTT
43035 ATTCAAAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (17 bp):
TATTTTTTATTTGTATG
Found at i:43077 original size:14 final size:15
Alignment explanation
Indices: 43058--43086 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43048 TTATGAGAAC
43058 TTAAATTTCA-AAAT
1 TTAAATTTCATAAAT
43072 TTAAATTTCATAAAT
1 TTAAATTTCATAAAT
43087 AGTGTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATTTCATAAAT
Found at i:43186 original size:13 final size:13
Alignment explanation
Indices: 43168--43192 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43158 ATTCATTGTT
43168 TTTTTATTTTTTA
1 TTTTTATTTTTTA
43181 TTTTTATTTTTT
1 TTTTTATTTTTT
43193 CATGGTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:48198 original size:96 final size:97
Alignment explanation
Indices: 48076--48271 Score: 376
Period size: 97 Copynumber: 2.0 Consensus size: 97
48066 GACTTAAAAG
48076 TTTGGGCTAGGGTTTAAATGTTTGTATTGGGCTGTTTATATTTT-GGCTATGGTTTAAAATTTGG
1 TTTGGGCTAGGGTTTAAATGTTTGTATTGGGCTGTTTATATTTTGGGCTATGGTTTAAAATTTGG
*
48140 GTCTGAATTGGTAAACAAAAATGAACTGTTTA
66 GTCTGAATTGGTAAACAAAAATGAACGGTTTA
48172 TTTGGGCTAGGGTTTAAATGTTTGTATTGGGCTGTTTATATTTTGGGCTATGGTTTAAAATTTGG
1 TTTGGGCTAGGGTTTAAATGTTTGTATTGGGCTGTTTATATTTTGGGCTATGGTTTAAAATTTGG
48237 GTCTGAATTGGTAAACAAAAATGAACGGTTTA
66 GTCTGAATTGGTAAACAAAAATGAACGGTTTA
48269 TTT
1 TTT
48272 TGGTTTTATT
Statistics
Matches: 98, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
96 44 0.45
97 54 0.55
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.43
Consensus pattern (97 bp):
TTTGGGCTAGGGTTTAAATGTTTGTATTGGGCTGTTTATATTTTGGGCTATGGTTTAAAATTTGG
GTCTGAATTGGTAAACAAAAATGAACGGTTTA
Found at i:49026 original size:178 final size:177
Alignment explanation
Indices: 48442--49018 Score: 793
Period size: 176 Copynumber: 3.3 Consensus size: 177
48432 TGCCCTTTCT
* * * * *
48442 GATCTTCTCCATAGCCGGTACATGGAGATAGGATCTGTAATTTTCAGCCCGTTACCCTACTACTT
1 GATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTACTT
* *
48507 AGGGGGTTAAGGCTCGTATCTTCAACCTACTCTCTTGCTACCTCAGAGAGATAAGGCCGGTAGCT
66 AGGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCT
48572 TAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATCTTC
131 TAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATCTTC
* * * * *
48619 GATCTGTTCCATAGTCGATACAT-GAGATAATATCTACAATTTTCAGCCTGTTACCCTACTGCTT
1 GATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTACTT
*
48683 AGGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAAATAAGGCCGGTGGCT
66 AGGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCT
* * **
48748 TAAATTTGCTTCATAGTTGATACATGGAGATAAGACTCGCCATCTTC
131 TAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATCTTC
* * * * *
48795 GATCTGCTCCATAGTCGATACATGGAGATAAAATCTATAATTTTCAGTCTGCTT-CCTTGCTACT
1 GATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTG-TTACCCTACTACT
** * * ***
48859 TCAGGAAGATAAGACTCGTATCTTCAACCTGCTCTCTTGCTACC-CTAGAGAGATAAGGTTAGTG
65 T-AGGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTC-AGAGAGATAAGGCCGGTG
* * *
48923 GCTAAAATCTGCTCCATAGCCGGTACATAGAGATAAGACTCGCCAT-TTC
128 GCTTAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATCTTC
*
48972 TGATCTGCTCCATAGCCGATCCATGGAGATAAGATCTATAATTTTCA
1 -GATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCA
49019 ATCTGCTTTG
Statistics
Matches: 353, Mismatches: 42, Indels: 9
0.87 0.10 0.02
Matches are distributed among these distances:
176 162 0.46
177 55 0.16
178 136 0.39
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (177 bp):
GATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTACTT
AGGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCCGGTGGCT
TAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATCTTC
Found at i:50393 original size:105 final size:105
Alignment explanation
Indices: 50234--50501 Score: 459
Period size: 105 Copynumber: 2.6 Consensus size: 105
50224 TGTATATAAA
** *
50234 AGGGGTTGCTGTGTGCTGATT-CCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
50297 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
50338 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
50403 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
50443 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
50502 ATAACGGTTA
Statistics
Matches: 155, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
104 19 0.12
105 135 0.87
106 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (105 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:57626 original size:27 final size:27
Alignment explanation
Indices: 57588--57641 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
57578 AAATGTGAAA
*
57588 AGGGGGTTGCTATGTGCTGATTCCCCG
1 AGGGGGTTGCTAAGTGCTGATTCCCCG
*
57615 AGGGGTTTGCTAAGTGCTGATTCCCCG
1 AGGGGGTTGCTAAGTGCTGATTCCCCG
57642 GTTCATTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.13, C:0.22, G:0.35, T:0.30
Consensus pattern (27 bp):
AGGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:57652 original size:105 final size:105
Alignment explanation
Indices: 57523--57779 Score: 437
Period size: 105 Copynumber: 2.4 Consensus size: 105
57513 GGGTTGCTGT
*
57523 GTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTTTGAAATGTGAAA
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTTTGAAATGTGAAA
57588 AGGGGGTTGCTATGTGCTGATT-CCCCGAGGGGTTTGCTAA
66 A-GGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTTGCTAA
* *
57628 GTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGTGAT-ATCCACCATATCTTTGAAATGTGAA
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TGATCCACCATATCTTTGAAATGTGAA
57692 AAGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTTGCTAA
65 AAGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTTGCTAA
* *
57733 GTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCA
57780 ATAACGGTTA
Statistics
Matches: 142, Mismatches: 7, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
104 20 0.14
105 121 0.85
106 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.31
Consensus pattern (105 bp):
GTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTTTGAAATGTGAAA
AGGGGTTGCTATGTGCTGATTCCCCCGAGGGGTTTGCTAA
Found at i:57747 original size:27 final size:27
Alignment explanation
Indices: 57693--57745 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
57683 AAATGTGAAA
*
57693 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
57720 AGGGGTTTGCTAAGTGCTGATTCCCC
1 AGGGG-TTGCTAAGTGCTGATTCCCC
57746 GATTCAGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.13, C:0.25, G:0.32, T:0.30
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Done.